


Second Phase AU

by silentsenpai



Category: The Maze Runner Series - All Media Types
Genre: M/M, alternative universe for second phase of the the trials, heavy smut, if you're not into knots don't read this, omegaverse somewhat
Language: English
Status: Completed
Published: 2015-11-24
Updated: 2015-11-24
Packaged: 2018-05-03 03:45:52
Rating: Explicit
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 1,950
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/5275256
Author URL: https://archiveofourown.org/users/silentsenpai/pseuds/silentsenpai
Summary: <blockquote class="userstuff">
              <p>“Aris still didn’t seem very winded. ‘Well, actually I have two ideas. One is I think these people— WICKED, whoever they are—are trying to weed out the best of both groups to use us somehow. Maybe even breed us or something like that.’<br/>‘What?’ Thomas was so surprised he almost forgot about the screaming. He couldn’t believe anyone would be so sick. ‘Breed us? Come on.’” (Scorch Trials)<br/>If only if Thomas knew he was so, so, so wrong.</p>
            </blockquote>





	Second Phase AU

**Author's Note:**

  * Inspired by [Legacy](https://archiveofourown.org/works/4425641) by [RoseKnightRed](https://archiveofourown.org/users/RoseKnightRed/pseuds/RoseKnightRed). 



> If you don't like omegaverse, then this isn't for you! It isn't out right stated in the text, but it is implied. Thanks!

Thomas never remembered having a room that looked so blank, lacking of so much life. Even in the Glade, there was life everywhere— there were forests, gardens, so much color, even if the life was horrible—and now he was stuck in a room with no one but himself. Luckily, Thomas could deal with isolation, but it wasn’t himself he was worried about.

It was Minho.

Even if he only knew Minho for a week or two, he knew that the guy needed his interaction. Unlike Thomas, he was an extrovert, not an introvert. He softly chuckled for a moment, imagining the amount of struggle that the Asian was probably putting up— after all, no one from Group A was really happy after the amount of surgery everyone was forced to go through. He couldn’t explain it, but after the surgery he felt different, like the doctors of WICKED switched his organs around; making Thomas nearly vomit on the white tiled floor. He began taking deep breaths, thinking of the Gladers: Newt, Winston, Minho, Chuck...

Chuck.

Thinking about the prepubescent boy still made Thomas’s eyes water and his throat tighten, making his fists clench with anger when he thought back to the way Gally stabbed him, when Thomas almost killed the dark-haired boy with only his fists. If it wasn’t for the others, he probably would’ve been dead, Thomas assumed.

But then a noise came about. A machine-like groan came throughout the room, causing him to get up and move quickly towards the walls; not noticing the metallic shield of the windows of the room to loosen and raise, allowing Thomas to see another room beyond his. It was the exact same: the tiles, the equipment, the tables, the walls—they were all the same.

Just white.

Blank.

Lifeless.

Thomas sighed with relief, noticing there was nothing in the room that was life threatening. He scoffed at the thought, and snorted, now seeing a familiar figure laying on the table with clean and freshly-pressed dark grey pants and nothing else. Thomas immediately recognized who it was, it was Minho, the teen who led everyone out of the maze, no matter what anyone else said about his help.

At this moment, Minho noticed him from the other side. He slowly sat up waving, and smiled, giving Thomas a sign that the smile was sarcastic and the guy didn’t enjoy this one bit. And honestly, Thomas didn’t blame him; he didn’t like this predicament either. He had no idea what was going to happen and if he was honest to himself, Thomas was scared.

Would it be worse than Grievers? Would it be less? What variables would be put into play? So many things rushed through his head, so many thoughts running through his brain; the stress of the trials finally catching up to him. But soon, the stress was too much for him to handle and Thomas shoved the center table over—effectively catching Minho’s attention.

Fingers ran through Thomas’s dark brown hair, his breath becoming stagnant and his muscles becoming tense, tense, tenser. He heard a knock on the window, knowing Minho was trying to catch his attention, but he was busy, busy stressing, not acknowledging the now banging on the window.

 _“Thomas! Thomas, you shank, look at me!”_ Minho was screaming at the top of his lungs, but only a whisper getting through the thick, almost soundproof glass. _“Don’t you let those shucking klunkheads get into your head! Come on Thomas, come on!”_

Thomas layed a hand against the glass, mirroring Minho’s own. He looked into the dark eyes of the Keeper, reading his lips loud and clear—you alright, you shank?—and he breathed deeply before nodding slowly.

“Are you?” He asked.

_Hah, Greenie, I’m downright shucking pissed. I don’t like being isolated._

“I don’t quite like it either. I keep wondering about the second phase,” Thomas admitted to the other runner, forcing himself to strain a smile. “We were free, but now we’re not. We’re like pets, like animals,” And after that, Minho didn’t reply for a while, making Thomas think he was thinking about his comment.

A knock on the glass brought him back to his senses.

_Don’t you worry, you stupid shank. We’ll get out of here, whether these shucking doctors like or not._

And then, walking through Minho’s doors, came more of the white coated doctors sliding along a surgery table and a syringe. Thomas had seen it before, it was what they used before putting him through that awful surgery, and he started banging on the window.

“Minho! Minho! Don’t let them take you!” Minho looked at Thomas, nodding, and Thomas continued screaming at the top of his lungs. “They’ll change you, like they shucking changed me! Minho! Minho, something isn’t right here!”

The metallic shield began closing, and that was the last time he saw Minho for two weeks. The first few days were filled with sedates and in-and-out experiences, his mind going almost insane for not knowing what they did to his friend, to Minho. Did they erase even more of his brain? Did they... Did they kill him? Thomas didn’t know, and it almost killed him, knowing that he was helpless against the enclosed jail that surrounded him.

But after those first few days, stress, experiences, sobbing, and experiments were the only things on the agenda for Thomas. He was a complete wreck without Minho and the others—he acknowledged that. His entire being screamed for the Keeper, not caring that he was thinking of romantic thoughts about him.

And then he slept.

* * *

Minho was downright furious.

All of his vision encompassed the color red, just red, red, red, and the need for punishment when he found out that those shucks, those shucking creators of the Grievers, had experimented on Thomas. Out of all the lines to cross, that was one Minho didn’t expect for them to cross, and it wasn’t doing well for his mental status. The room of his was torn apart, and the only thing that wasn’t demolished was that stupid metal wall.  
He needed to talk to Thomas. Was he alright? What exactly had they done to him? His brain kept thinking of what they might’ve done to the other runner, and what they could do to reverse it, but nothing was coming up, and nothing didn’t satisfy him. Unknown to Thomas, Minho was always curious and fondly attracted to the other male when he came up in the Box; he decided not to say anything, thinking he was just another Greenie, just another shank.

Oh, just how wrong he was.

When Thomas saved his life in the maze, hell, when Thomas found about the Griever-Hole, Minho could’ve kissed him. Of course that would’ve been weird, and maybe a little bit satisfying, but it wasn’t the right time or place. Also, he was pretty damn sure that Thomas had freakin’ feelings for that girl shank Teresa. He tried not to think about it—it clenched his main organ— and he didn’t like that, either.

But back in the present, the day had been slow, just like any other day. The day before he was experimented on again, and was ‘cleared from testing’, whatever the shuck that meant. But Minho was ready to get out of this hell hole, to see Thomas and the others, and to hopefully punch a person from WICKED in the face.

Creak.

Minho looked up, seeing the ventilation open. Nothing was coming out, but there was this smell in the air.

A good smell.

A really, really, delicious tasting smell.

Minho’s body began to get hot, and hotter; no longer feeling cold from the high air conditioning.

Sweat.

Hot.

Red.

His vision was red, once again. And then he thought of Thomas. Thomas.

When cold hands grabbed his shoulders, he snarled, all of his pent up anger and fury raging outside of his system now; struggling against the monsters who dragged him down a hallway with his hands behind his back. They eventually reached a door that had a metal plate that was inscribed “A-2” beside the doorway.

He was shoved into the room.

And then he saw Thomas.

* * *

 

Thomas almost cried when he saw Minho. The Keeper was in nothing but tight pants, leaving nothing unknown to his own eyes, more slick producing when he saw the raging bulge in his pants; the sweat dripping off of Minho making him whimper. He would’ve spoken if he could have, but all he could sounds he could make were whimpers and whines.

But if the sight of the male himself wasn’t enough to make Thomas to go into a sexual craze, it was the pheromones that Minho produced. He felt more slick literally pouring from his ass, adding to the thick puddle on the floor beneath him. It had a disgusting feel, but at the moment he didn’t really care. All he wanted Minho.

But then he saw Minho’s lips moving.

“—hey, Thomas, you in there?” His voice was lower than normal, quieter. “I’m gonna help you out, okay you shank?”

A whine passed through his lips.

“M.. Min... O,” Thomas strained. “Experiment. They. Something wrong.” Words were only coming out in one or two, but luckily, the message was put across between the two boys. Thomas noticed Minho’s clenched jaw, one side thinking it was appealing, but other sane side knowing that the words had made him upset—really upset.

A few seconds passed, and Minho spoke once again. “I know, Greenie. I’ll think of a way to reverse it, promise it, okay?” Thomas nodded. “But for now, I’m gonna help you out, alright?” Thomas watched as Minho’s pants dropped, his swollen cock uncoiling from the clothed pressure; a wanton whine forcefully spilling out of his mouth.

It was then when his mind completely went primal.

He could feel the gentle and soft kisses against his throat and neck and collarbone, fingers trailing down his abdomen, easing into his asshole. Moans kept rushing through up, up, up, and his hips bucked up to the dominant male’s fingers, wanting something else besides those slim digits. Thomas wanted that cock to breed him, to fill him up with his thick cum, something he would’ve never thought of before. But now, under the influence of pheromones, Thomas could feel the sexual and mental need for Minho to take him as his, to be his, and to give him children.

If he was in his right mind, he would be a little freaked out. No offense to Minho, of course.

The very next second, however, Minho was balls deep inside him. The feeling was marvelous and incredibly filling, a pleasant hum going throughout his body. In and out Minho went, filling him up with intense pleasure to his prostate, going faster and deeper, until he couldn’t move anymore; a huge intrusion filling him at the base of his hole.

And then he came. The tension snapped like a high strung string, and a white light blinded his vision, not being able to control the shaking of his hips or the inside throbbing around the cock and the overwhelming amounts of cum. By the time he was done, he was being lifted from the table (when did he get there?) and onto the other side.

“... Minho? What happened?”

Minho was looking at the huge mess. “We had sex, shank. And a pretty shucking messy one we did, too. It’s from the experiments, I bet.”

The only thing Thomas could do right now, however, was lie down and fall asleep.

And neither of them knew it, but maybe this was the weird start to a relationship. Just maybe.


End file.
